Document Detail


Effects of column and gradient lengths on peak capacity and peptide identification in nanoflow LC-MS/MS of complex proteomic samples.
MedLine Citation:
PMID:  23197307     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Reversed-phase liquid chromatography is the most commonly used separation method for shotgun proteomics. Nanoflow chromatography has emerged as the preferred chromatography method for its increased sensitivity and separation. Despite its common use, there are a wide range of parameters and conditions used across research groups. These parameters have an effect on the quality of the chromatographic separation, which is critical to maximizing the number of peptide identifications and minimizing ion suppression. Here we examined the relationship between column lengths, gradient lengths, peptide identifications, and peptide peak capacity. We found that while longer column and gradient lengths generally increase peptide identifications, the degree of improvement is dependent on both parameters and is diminished at longer column and gradients. Peak capacity, in comparison, showed a more linear increase with column and gradient lengths. We discuss the discrepancy between these two results and some of the considerations that should be taken into account when deciding on the chromatographic conditions for a proteomics experiment.
Authors:
Edward J Hsieh; Michael S Bereman; Stanley Durand; Gary A Valaskovic; Michael J MacCoss
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-11-30
Journal Detail:
Title:  Journal of the American Society for Mass Spectrometry     Volume:  24     ISSN:  1879-1123     ISO Abbreviation:  J. Am. Soc. Mass Spectrom.     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-24     Completed Date:  2013-07-01     Revised Date:  2014-01-09    
Medline Journal Info:
Nlm Unique ID:  9010412     Medline TA:  J Am Soc Mass Spectrom     Country:  United States    
Other Details:
Languages:  eng     Pagination:  148-53     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Caenorhabditis elegans Proteins / analysis,  chemistry
Chromatography, Liquid / instrumentation*,  methods
Nanotechnology / instrumentation*
Peptide Mapping / instrumentation*,  methods
Proteome / analysis,  chemistry
Proteomics / instrumentation*,  methods
Tandem Mass Spectrometry / methods*
Grant Support
ID/Acronym/Agency:
P41 RR011823/RR/NCRR NIH HHS; P41GM103533/GM/NIGMS NIH HHS; R01 DK069386/DK/NIDDK NIH HHS; R01DK069386/DK/NIDDK NIH HHS; S10 RR021026/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Caenorhabditis elegans Proteins; 0/Proteome
Comments/Corrections

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